Starting phenix.real_space_refine
on Thu Jun 12 23:46:53 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8g5j_29746/06_2025/8g5j_29746_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g5j_29746/06_2025/8g5j_29746.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g5j_29746/06_2025/8g5j_29746.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g5j_29746/06_2025/8g5j_29746.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g5j_29746/06_2025/8g5j_29746_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g5j_29746/06_2025/8g5j_29746_neut.cif"
  }
  resolution = 2.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      40      5.49       5
     S      80      5.16       5
     C    9131      2.51       5
     N    2562      2.21       5
     O    2731      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14544
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 941, 7369
          Classifications: {'peptide': 941}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 60, 'TRANS': 880}
          Chain breaks: 5
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 143
          Unresolved non-hydrogen angles: 187
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 4, 'ASP:plan': 5, 'GLU:plan': 3, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 94
    Chain: "B"
      Number of atoms: 3188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 3188
          Classifications: {'peptide': 398}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 18, 'TRANS': 379}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "C"
      Number of atoms: 3168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 400, 3168
          Classifications: {'peptide': 400}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 18, 'TRANS': 381}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "P"
      Number of atoms: 413
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 19, 393
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 19, 393
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 419
    Chain: "T"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 406
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" P  A DA P  28 " occ=0.50
      ... (38 atoms not shown)
      pdb=" C4 B DA P  28 " occ=0.50
    residue:
      pdb=" P    DG T   3 " occ=0.50
      ... (20 atoms not shown)
      pdb=" C4   DG T   3 " occ=0.50
  Time building chain proxies: 9.54, per 1000 atoms: 0.66
  Number of scatterers: 14544
  At special positions: 0
  Unit cell: (102.424, 102.424, 145.376, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      80     16.00
     P      40     15.00
     O    2731      8.00
     N    2562      7.00
     C    9131      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.94
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3242

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 10 sheets defined
      41.1% alpha, 12.2% beta
      17 base pairs and 32 stacking pairs defined.
    Time for finding SS restraints: 4.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 100 through 109
      removed outlier: 3.509A  pdb=" N   GLU A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 159
      Proline residue:  A 149  - end of helix
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 6.890A  pdb=" N   GLU A 280 " --> pdb=" O   HIS A 277 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   TYR A 282 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A 283 " --> pdb=" O   GLU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 303
      removed outlier: 3.725A  pdb=" N   GLY A 303 " --> pdb=" O   MET A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 316
    Processing helix  chain 'A' and resid 355 through 364
    Processing helix  chain 'A' and resid 381 through 388
    Processing helix  chain 'A' and resid 388 through 418
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'A' and resid 420 through 431
      removed outlier: 4.063A  pdb=" N   LEU A 424 " --> pdb=" O   HIS A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 471
      removed outlier: 3.501A  pdb=" N   ARG A 443 " --> pdb=" O   GLN A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 475
      removed outlier: 4.007A  pdb=" N   SER A 475 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 472 through 475'
    Processing helix  chain 'A' and resid 537 through 548
    Processing helix  chain 'A' and resid 551 through 556
      removed outlier: 4.041A  pdb=" N   THR A 555 " --> pdb=" O   LYS A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 577
    Processing helix  chain 'A' and resid 597 through 604
      removed outlier: 4.002A  pdb=" N   LYS A 601 " --> pdb=" O   ARG A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 777
    Processing helix  chain 'A' and resid 786 through 810
      removed outlier: 4.719A  pdb=" N   PHE A 800 " --> pdb=" O   LYS A 796 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   TRP A 801 " --> pdb=" O   MET A 797 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LYS A 806 " --> pdb=" O   ARG A 802 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   ARG A 807 " --> pdb=" O   ASN A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 827
      removed outlier: 3.597A  pdb=" N   ILE A 826 " --> pdb=" O   PRO A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 853
      removed outlier: 4.166A  pdb=" N   ARG A 853 " --> pdb=" O   ILE A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 874 through 878
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 903 through 908
    Processing helix  chain 'A' and resid 914 through 922
    Processing helix  chain 'A' and resid 930 through 939
      removed outlier: 3.503A  pdb=" N   THR A 938 " --> pdb=" O   LYS A 934 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL A 939 " --> pdb=" O   THR A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 954
      removed outlier: 4.629A  pdb=" N   GLY A 952 " --> pdb=" O   ILE A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 971
    Processing helix  chain 'A' and resid 973 through 984
      removed outlier: 4.264A  pdb=" N   LYS A 981 " --> pdb=" O   GLU A 977 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ALA A 982 " --> pdb=" O   ALA A 978 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLN A 983 " --> pdb=" O   ALA A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 988
    Processing helix  chain 'A' and resid 1057 through 1066
      removed outlier: 4.029A  pdb=" N   LEU A1061 " --> pdb=" O   MET A1057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1092 through 1124
      removed outlier: 3.762A  pdb=" N   VAL A1101 " --> pdb=" O   VAL A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1168
    Processing helix  chain 'A' and resid 1216 through 1221
      removed outlier: 3.624A  pdb=" N   ASP A1219 " --> pdb=" O   GLU A1216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 77
    Processing helix  chain 'B' and resid 87 through 94
    Processing helix  chain 'B' and resid 100 through 119
    Processing helix  chain 'B' and resid 185 through 192
    Processing helix  chain 'B' and resid 192 through 200
      removed outlier: 3.515A  pdb=" N   VAL B 200 " --> pdb=" O   CYS B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 265
    Processing helix  chain 'B' and resid 269 through 271
      No H-bonds generated for 'chain 'B' and resid 269 through 271'
    Processing helix  chain 'B' and resid 308 through 315
    Processing helix  chain 'B' and resid 319 through 323
    Processing helix  chain 'B' and resid 342 through 354
    Processing helix  chain 'B' and resid 394 through 409
      removed outlier: 4.062A  pdb=" N   VAL B 398 " --> pdb=" O   GLU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 435
    Processing helix  chain 'B' and resid 444 through 448
      removed outlier: 3.918A  pdb=" N   LEU B 448 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 485
    Processing helix  chain 'C' and resid 68 through 76
    Processing helix  chain 'C' and resid 88 through 93
    Processing helix  chain 'C' and resid 100 through 119
    Processing helix  chain 'C' and resid 185 through 192
    Processing helix  chain 'C' and resid 192 through 200
      removed outlier: 3.794A  pdb=" N   ASP C 198 " --> pdb=" O   VAL C 194 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU C 199 " --> pdb=" O   ASN C 195 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL C 200 " --> pdb=" O   CYS C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 246
      No H-bonds generated for 'chain 'C' and resid 244 through 246'
    Processing helix  chain 'C' and resid 247 through 266
      removed outlier: 4.158A  pdb=" N   PHE C 266 " --> pdb=" O   TRP C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 271
      No H-bonds generated for 'chain 'C' and resid 269 through 271'
    Processing helix  chain 'C' and resid 308 through 315
    Processing helix  chain 'C' and resid 318 through 323
      removed outlier: 3.982A  pdb=" N   LEU C 322 " --> pdb=" O   ASN C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 342 through 354
    Processing helix  chain 'C' and resid 391 through 409
    Processing helix  chain 'C' and resid 424 through 435
    Processing helix  chain 'C' and resid 444 through 451
      removed outlier: 3.584A  pdb=" N   LEU C 448 " --> pdb=" O   THR C 444 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 469 through 484
      removed outlier: 4.590A  pdb=" N   ASP C 473 " --> pdb=" O   SER C 469 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187
      removed outlier: 3.808A  pdb=" N   TRP A 175 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TRP A 220 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU A 211 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLU A 200 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU A 195 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   GLN A 264 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   LEU A 292 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   VAL A 266 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438
      removed outlier: 4.689A  pdb=" N   TYR A 837 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1130 through 1133
    Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127
      removed outlier: 6.294A  pdb=" N   PHE B 126 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 8.560A  pdb=" N   ILE B 211 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ILE B 300 " --> pdb=" O   ASP B 341 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   LYS B 297 " --> pdb=" O   PHE B 293 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   PHE B 293 " --> pdb=" O   LYS B 297 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   LEU B 299 " --> pdb=" O   TYR B 291 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   TYR B 291 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASN B 305 " --> pdb=" O   LYS B 285 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   LYS B 285 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134
    Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325
    Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 415
      removed outlier: 7.157A  pdb=" N   VAL B 383 " --> pdb=" O   TRP B 414 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   ALA B 384 " --> pdb=" O   VAL B 441 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   VAL B 443 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   ASP B 386 " --> pdb=" O   VAL B 443 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127
      removed outlier: 6.263A  pdb=" N   PHE C 126 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 8.526A  pdb=" N   ILE C 211 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE C 300 " --> pdb=" O   ASP C 341 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   LEU C 299 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   TYR C 291 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326
    Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415
      removed outlier: 6.865A  pdb=" N   VAL C 383 " --> pdb=" O   TRP C 414 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ALA C 384 " --> pdb=" O   VAL C 441 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   VAL C 443 " --> pdb=" O   ALA C 384 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ASP C 386 " --> pdb=" O   VAL C 443 " (cutoff:3.500A)

    570 hydrogen bonds defined for protein.
    1635 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 5.14

  Time building geometry restraints manager: 4.55 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 4473
        1.34 -     1.46: 2636
        1.46 -     1.58: 7664
        1.58 -     1.70: 79
        1.70 -     1.82: 126
  Bond restraints: 14978
  Sorted by residual:
  bond pdb=" P    DC T   4 "
       pdb=" OP2  DC T   4 "
    ideal  model  delta    sigma   weight residual
    1.480  1.621 -0.141 2.00e-02 2.50e+03 4.96e+01
  bond pdb=" C2'  DG T   3 "
       pdb=" C1'  DG T   3 "
    ideal  model  delta    sigma   weight residual
    1.525  1.438  0.087 2.00e-02 2.50e+03 1.90e+01
  bond pdb=" C1'  DA P  15 "
       pdb=" N9   DA P  15 "
    ideal  model  delta    sigma   weight residual
    1.460  1.381  0.079 2.00e-02 2.50e+03 1.56e+01
  bond pdb=" C1'  DG P  16 "
       pdb=" N9   DG P  16 "
    ideal  model  delta    sigma   weight residual
    1.460  1.382  0.078 2.00e-02 2.50e+03 1.52e+01
  bond pdb=" C1'  DG T  13 "
       pdb=" N9   DG T  13 "
    ideal  model  delta    sigma   weight residual
    1.460  1.387  0.073 2.00e-02 2.50e+03 1.33e+01
  ... (remaining 14973 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.44: 20371
        5.44 -    10.87: 90
       10.87 -    16.31: 8
       16.31 -    21.74: 0
       21.74 -    27.18: 1
  Bond angle restraints: 20470
  Sorted by residual:
  angle pdb=" C3'  DG T   3 "
        pdb=" O3'  DG T   3 "
        pdb=" P    DC T   4 "
      ideal   model   delta    sigma   weight residual
     120.20   93.02   27.18 1.50e+00 4.44e-01 3.28e+02
  angle pdb=" C4'  DG T   3 "
        pdb=" C3'  DG T   3 "
        pdb=" O3'  DG T   3 "
      ideal   model   delta    sigma   weight residual
     110.00  125.79  -15.79 1.50e+00 4.44e-01 1.11e+02
  angle pdb=" O3'  DG T   3 "
        pdb=" C3'  DG T   3 "
        pdb=" C2'  DG T   3 "
      ideal   model   delta    sigma   weight residual
     111.50   96.44   15.06 1.50e+00 4.44e-01 1.01e+02
  angle pdb=" N   PRO C 137 "
        pdb=" CA  PRO C 137 "
        pdb=" C   PRO C 137 "
      ideal   model   delta    sigma   weight residual
     113.65  100.84   12.81 1.35e+00 5.49e-01 9.00e+01
  angle pdb=" C3'  DC T   2 "
        pdb=" O3'  DC T   2 "
        pdb=" P    DG T   3 "
      ideal   model   delta    sigma   weight residual
     120.20  107.81   12.39 1.50e+00 4.44e-01 6.83e+01
  ... (remaining 20465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.66: 8082
       28.66 -    57.32: 668
       57.32 -    85.97: 81
       85.97 -   114.63: 0
      114.63 -   143.29: 3
  Dihedral angle restraints: 8834
    sinusoidal: 3819
      harmonic: 5015
  Sorted by residual:
  dihedral pdb=" CD  ARG A 102 "
           pdb=" NE  ARG A 102 "
           pdb=" CZ  ARG A 102 "
           pdb=" NH1 ARG A 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -69.84   69.84     1      1.00e+01 1.00e-02 6.29e+01
  dihedral pdb=" CD  ARG B 257 "
           pdb=" NE  ARG B 257 "
           pdb=" CZ  ARG B 257 "
           pdb=" NH1 ARG B 257 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -57.20   57.20     1      1.00e+01 1.00e-02 4.40e+01
  dihedral pdb=" CD  ARG B 154 "
           pdb=" NE  ARG B 154 "
           pdb=" CZ  ARG B 154 "
           pdb=" NH1 ARG B 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   55.71  -55.71     1      1.00e+01 1.00e-02 4.19e+01
  ... (remaining 8831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.236: 2195
       0.236 -    0.472: 24
       0.472 -    0.708: 8
       0.708 -    0.944: 0
       0.944 -    1.179: 1
  Chirality restraints: 2228
  Sorted by residual:
  chirality pdb=" P    DC T   4 "
            pdb=" OP1  DC T   4 "
            pdb=" OP2  DC T   4 "
            pdb=" O5'  DC T   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.53   -1.18 2.00e-01 2.50e+01 3.48e+01
  chirality pdb=" P    DC T   2 "
            pdb=" OP1  DC T   2 "
            pdb=" OP2  DC T   2 "
            pdb=" O5'  DC T   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.98   -0.64 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" P    DA P  10 "
            pdb=" OP1  DA P  10 "
            pdb=" OP2  DA P  10 "
            pdb=" O5'  DA P  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.95   -0.60 2.00e-01 2.50e+01 9.15e+00
  ... (remaining 2225 not shown)

  Planarity restraints: 2497
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 102 "   -1.036 9.50e-02 1.11e+02   4.64e-01 1.30e+02
        pdb=" NE  ARG A 102 "    0.061 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 102 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 102 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 102 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 257 "   -0.923 9.50e-02 1.11e+02   4.14e-01 1.04e+02
        pdb=" NE  ARG B 257 "    0.055 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 257 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 257 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 257 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 154 "   -0.904 9.50e-02 1.11e+02   4.05e-01 9.96e+01
        pdb=" NE  ARG B 154 "    0.054 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 154 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 154 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 154 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 2494 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 283
        2.67 -     3.22: 13525
        3.22 -     3.78: 23408
        3.78 -     4.34: 31799
        4.34 -     4.90: 51352
  Nonbonded interactions: 120367
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 892 "
            pdb=" OG  SER A1181 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" NH2 ARG B  75 "
            pdb=" O   GLY B  81 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OG1 THR A 885 "
            pdb=" O   ASP A1186 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   ASP A 491 "
            pdb=" NH2 ARG A 574 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" C2'  DG T   3 "
            pdb=" P    DC T   4 "
     model   vdw
     2.229 3.040
  ... (remaining 120362 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 68 through 104 or (resid 105 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name CD )) or resid 106 through 136 or (r \ 
esid 137 and (name N or name CA or name C or name O )) or resid 138 through 219  \ 
or resid 229 through 283 or (resid 284 through 285 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 286 through 355 or resid 368 through 485))
  selection = (chain 'C' and (resid 68 through 161 or (resid 169 through 178 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 179 through 219 or resid 229 th \ 
rough 485))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.090
  Set scattering table:                    0.140
  Process input model:                     38.990
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.141  14978  Z= 0.318
  Angle     :  1.039  27.179  20470  Z= 0.600
  Chirality :  0.076   1.179   2228
  Planarity :  0.021   0.464   2497
  Dihedral  : 19.274 143.288   5592
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  5.84 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 25.14 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.20), residues: 1713
  helix:  1.05 (0.21), residues: 658
  sheet:  0.29 (0.33), residues: 228
  loop : -1.78 (0.20), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 607 
 HIS   0.016   0.001   HIS C 309 
 PHE   0.039   0.001   PHE A 961 
 TYR   0.018   0.001   TYR C 291 
 ARG   0.024   0.001   ARG A 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14209 (  614)
  hydrogen bonds       : angle       6.84950 ( 1723)
  covalent geometry    : bond        0.00586 (14978)
  covalent geometry    : angle       1.03933 (20470)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 178
  time to evaluate  : 1.668 
Fit side-chains
REVERT: A   87 ILE cc_start: 0.2050 (OUTLIER) cc_final: 0.1459 (pp)
REVERT: A  215 ILE cc_start: 0.7484 (pt) cc_final: 0.7283 (pt)
REVERT: B  329 LYS cc_start: 0.7431 (ptmm) cc_final: 0.7196 (ptmt)
REVERT: B  460 THR cc_start: 0.7615 (p) cc_final: 0.7225 (p)
REVERT: C  397 GLN cc_start: 0.7095 (mp10) cc_final: 0.6506 (mp10)
  outliers start: 32
  outliers final: 12
  residues processed: 207
  average time/residue: 1.1945
  time to fit residues: 274.7459
Evaluate side-chains
  172 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 1.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 SER
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue  353 SER
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  485 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 148 optimal weight:    5.9990
   chunk 133 optimal weight:    0.9980
   chunk 74 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 137 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 102 optimal weight:    0.3980
   chunk 159 optimal weight:    2.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
A 144 GLN
A 550 GLN
A 761 ASN
A 811 GLN
A 843 GLN
A 894 GLN
A 922 GLN
A1059 ASN
A1089 GLN
A1110 HIS
A1222 GLN
B 133 HIS
B 187 HIS
B 272 ASN
C 250 GLN
C 279 GLN
C 309 HIS
C 330 ASN
C 404 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.183403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.129244 restraints weight = 41338.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 4.70
r_work: 0.3433 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3448
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3448
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  14978  Z= 0.211
  Angle     :  0.701  11.865  20470  Z= 0.362
  Chirality :  0.047   0.266   2228
  Planarity :  0.006   0.066   2497
  Dihedral  : 16.462 145.524   2313
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.95 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 24.11 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.20), residues: 1713
  helix:  1.16 (0.21), residues: 656
  sheet:  0.45 (0.32), residues: 238
  loop : -1.77 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 748 
 HIS   0.008   0.001   HIS A  84 
 PHE   0.019   0.002   PHE A 610 
 TYR   0.015   0.002   TYR C 291 
 ARG   0.013   0.001   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04816 (  614)
  hydrogen bonds       : angle       5.04668 ( 1723)
  covalent geometry    : bond        0.00491 (14978)
  covalent geometry    : angle       0.70075 (20470)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 166
  time to evaluate  : 1.550 
Fit side-chains
REVERT: A   87 ILE cc_start: 0.2598 (OUTLIER) cc_final: 0.1780 (pp)
REVERT: A  183 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5953 (pm20)
REVERT: A  372 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6626 (mt-10)
REVERT: A  484 TRP cc_start: 0.7950 (m-90) cc_final: 0.6914 (m-10)
REVERT: A  774 MET cc_start: 0.7227 (mmt) cc_final: 0.6999 (mmt)
REVERT: B  325 ARG cc_start: 0.7360 (mtm110) cc_final: 0.7104 (mtm180)
REVERT: B  421 MET cc_start: 0.6734 (pp-130) cc_final: 0.6432 (pp-130)
REVERT: C  355 GLN cc_start: 0.5054 (OUTLIER) cc_final: 0.3992 (pm20)
  outliers start: 57
  outliers final: 23
  residues processed: 203
  average time/residue: 1.1985
  time to fit residues: 269.9789
Evaluate side-chains
  177 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  235 THR
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  485 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 156 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   chunk 154 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 151 optimal weight:    1.9990
   chunk 129 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0870
   chunk 168 optimal weight:    0.9990
   chunk 114 optimal weight:    4.9990
   overall best weight:    0.7760

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  84 HIS
A 550 GLN
A 803 ASN
A1102 GLN
B 409 ASN
C 309 HIS
C 409 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.186240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.133203 restraints weight = 45040.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 4.90
r_work: 0.3467 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14978  Z= 0.137
  Angle     :  0.609   9.637  20470  Z= 0.316
  Chirality :  0.043   0.152   2228
  Planarity :  0.005   0.065   2497
  Dihedral  : 16.368 146.736   2307
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.30 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 24.59 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.20), residues: 1713
  helix:  1.26 (0.21), residues: 663
  sheet:  0.51 (0.33), residues: 238
  loop : -1.73 (0.21), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 748 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.014   0.001   PHE A 766 
 TYR   0.011   0.001   TYR A1108 
 ARG   0.013   0.001   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  614)
  hydrogen bonds       : angle       4.81469 ( 1723)
  covalent geometry    : bond        0.00306 (14978)
  covalent geometry    : angle       0.60916 (20470)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 165
  time to evaluate  : 1.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ILE cc_start: 0.2572 (OUTLIER) cc_final: 0.1771 (pp)
REVERT: A  108 GLN cc_start: 0.6794 (tt0) cc_final: 0.6456 (mt0)
REVERT: A  183 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5874 (pm20)
REVERT: A  372 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6540 (mt-10)
REVERT: A  603 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.4419 (ppp)
REVERT: A  910 MET cc_start: 0.7838 (mpp) cc_final: 0.7569 (mpt)
REVERT: A 1131 ILE cc_start: 0.4910 (OUTLIER) cc_final: 0.4125 (mt)
REVERT: B  314 MET cc_start: 0.8332 (ttm) cc_final: 0.8061 (mtp)
REVERT: B  325 ARG cc_start: 0.7418 (mtm110) cc_final: 0.7192 (mtm180)
REVERT: B  421 MET cc_start: 0.6702 (pp-130) cc_final: 0.6334 (pp-130)
REVERT: C  355 GLN cc_start: 0.4935 (OUTLIER) cc_final: 0.3914 (pm20)
REVERT: C  400 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6904 (tm-30)
  outliers start: 53
  outliers final: 23
  residues processed: 198
  average time/residue: 1.1170
  time to fit residues: 246.5076
Evaluate side-chains
  186 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  381 ILE
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  485 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 136 optimal weight:    0.5980
   chunk 143 optimal weight:    0.1980
   chunk 80 optimal weight:    4.9990
   chunk 124 optimal weight:    0.9980
   chunk 65 optimal weight:    0.3980
   chunk 151 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 148 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 394 GLN
A 550 GLN
A 564 GLN
A 803 ASN
A 828 HIS
** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 GLN
C 409 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.183858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131548 restraints weight = 36470.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 3.92
r_work: 0.3478 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14978  Z= 0.154
  Angle     :  0.622  13.489  20470  Z= 0.320
  Chirality :  0.043   0.261   2228
  Planarity :  0.005   0.064   2497
  Dihedral  : 16.328 146.826   2306
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.60 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 24.31 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.20), residues: 1713
  helix:  1.26 (0.21), residues: 663
  sheet:  0.63 (0.33), residues: 232
  loop : -1.74 (0.21), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 748 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.015   0.001   PHE C 403 
 TYR   0.018   0.002   TYR C 206 
 ARG   0.010   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03847 (  614)
  hydrogen bonds       : angle       4.77382 ( 1723)
  covalent geometry    : bond        0.00353 (14978)
  covalent geometry    : angle       0.62199 (20470)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 165
  time to evaluate  : 1.572 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.5809 (tpt) cc_final: 0.5602 (tpt)
REVERT: A  108 GLN cc_start: 0.6853 (tt0) cc_final: 0.6595 (mt0)
REVERT: A  183 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5775 (pm20)
REVERT: A  372 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6610 (mt-10)
REVERT: A  442 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8238 (mm-30)
REVERT: A  484 TRP cc_start: 0.7908 (m-90) cc_final: 0.6942 (m-10)
REVERT: A  603 MET cc_start: 0.4697 (OUTLIER) cc_final: 0.4471 (ppp)
REVERT: A  910 MET cc_start: 0.7796 (mpp) cc_final: 0.7500 (mpt)
REVERT: A 1131 ILE cc_start: 0.5012 (OUTLIER) cc_final: 0.4188 (mt)
REVERT: B  314 MET cc_start: 0.8382 (ttm) cc_final: 0.8135 (mtp)
REVERT: B  325 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7224 (mtm180)
REVERT: B  394 GLU cc_start: 0.7973 (tp30) cc_final: 0.7705 (tp30)
REVERT: B  421 MET cc_start: 0.6689 (pp-130) cc_final: 0.6147 (pp-130)
REVERT: B  460 THR cc_start: 0.7985 (p) cc_final: 0.7702 (p)
REVERT: C  355 GLN cc_start: 0.4971 (OUTLIER) cc_final: 0.3915 (pm20)
REVERT: C  400 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6832 (tm-30)
  outliers start: 61
  outliers final: 27
  residues processed: 207
  average time/residue: 1.5664
  time to fit residues: 359.0572
Evaluate side-chains
  189 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 155
  time to evaluate  : 1.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  381 ILE
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 145 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 155 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 138 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
A 803 ASN
A 911 HIS
A1214 GLN
B 261 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.181603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.128007 restraints weight = 37989.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 4.03
r_work: 0.3423 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3442
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14978  Z= 0.187
  Angle     :  0.661  12.858  20470  Z= 0.338
  Chirality :  0.045   0.198   2228
  Planarity :  0.005   0.070   2497
  Dihedral  : 16.367 147.127   2303
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.95 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 25.14 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.20), residues: 1713
  helix:  1.11 (0.20), residues: 666
  sheet:  0.57 (0.34), residues: 232
  loop : -1.78 (0.21), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 748 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.016   0.002   PHE A 749 
 TYR   0.013   0.002   TYR C 291 
 ARG   0.011   0.001   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  614)
  hydrogen bonds       : angle       4.86980 ( 1723)
  covalent geometry    : bond        0.00439 (14978)
  covalent geometry    : angle       0.66147 (20470)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 166
  time to evaluate  : 1.573 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6919 (tt0) cc_final: 0.6206 (mt0)
REVERT: A  183 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5899 (pm20)
REVERT: A  372 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6658 (mt-10)
REVERT: A  442 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8249 (mm-30)
REVERT: A  603 MET cc_start: 0.4731 (OUTLIER) cc_final: 0.4419 (ppp)
REVERT: A  780 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6782 (mt0)
REVERT: A  910 MET cc_start: 0.7862 (mpp) cc_final: 0.7588 (mpt)
REVERT: A  947 LYS cc_start: 0.5899 (tptt) cc_final: 0.5070 (ttmt)
REVERT: B  314 MET cc_start: 0.8466 (ttm) cc_final: 0.8248 (mtp)
REVERT: B  394 GLU cc_start: 0.8017 (tp30) cc_final: 0.7551 (tp30)
REVERT: B  421 MET cc_start: 0.6797 (pp-130) cc_final: 0.6305 (pp-130)
REVERT: B  460 THR cc_start: 0.8041 (p) cc_final: 0.7799 (p)
REVERT: C  355 GLN cc_start: 0.5052 (OUTLIER) cc_final: 0.3952 (pm20)
REVERT: C  400 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6911 (tm-30)
  outliers start: 59
  outliers final: 31
  residues processed: 209
  average time/residue: 1.1391
  time to fit residues: 265.2211
Evaluate side-chains
  196 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 158
  time to evaluate  : 1.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  442 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1212 ILE
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  381 ILE
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 150 optimal weight:    0.9990
   chunk 71 optimal weight:   10.0000
   chunk 167 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 169 optimal weight:    1.9990
   chunk 137 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 110 optimal weight:    0.8980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.183244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129636 restraints weight = 39022.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 4.10
r_work: 0.3448 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3455
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3455
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14978  Z= 0.150
  Angle     :  0.626  13.560  20470  Z= 0.320
  Chirality :  0.043   0.165   2228
  Planarity :  0.005   0.064   2497
  Dihedral  : 16.318 147.329   2303
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.65 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 25.07 %
    Favored  : 70.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.20), residues: 1713
  helix:  1.18 (0.20), residues: 666
  sheet:  0.57 (0.34), residues: 232
  loop : -1.76 (0.21), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 607 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.016   0.001   PHE A 766 
 TYR   0.012   0.001   TYR A 233 
 ARG   0.009   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03720 (  614)
  hydrogen bonds       : angle       4.80439 ( 1723)
  covalent geometry    : bond        0.00343 (14978)
  covalent geometry    : angle       0.62576 (20470)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 164
  time to evaluate  : 1.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6934 (tt0) cc_final: 0.6197 (mt0)
REVERT: A  120 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8684 (tp)
REVERT: A  183 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5904 (pm20)
REVERT: A  372 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6601 (mt-10)
REVERT: A  484 TRP cc_start: 0.7905 (m-90) cc_final: 0.6954 (m-10)
REVERT: A  780 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7106 (pt0)
REVERT: A  947 LYS cc_start: 0.5817 (tptt) cc_final: 0.5072 (ttmt)
REVERT: A 1121 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7465 (tm-30)
REVERT: A 1131 ILE cc_start: 0.5034 (OUTLIER) cc_final: 0.4233 (mt)
REVERT: B  256 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8006 (tp)
REVERT: B  314 MET cc_start: 0.8442 (ttm) cc_final: 0.8226 (mtp)
REVERT: B  394 GLU cc_start: 0.8009 (tp30) cc_final: 0.7503 (tp30)
REVERT: B  421 MET cc_start: 0.6732 (pp-130) cc_final: 0.6297 (pp-130)
REVERT: B  460 THR cc_start: 0.8020 (p) cc_final: 0.7783 (p)
REVERT: C  306 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6936 (mt)
REVERT: C  355 GLN cc_start: 0.4979 (OUTLIER) cc_final: 0.3879 (pm20)
REVERT: C  400 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6887 (tm-30)
  outliers start: 65
  outliers final: 34
  residues processed: 211
  average time/residue: 1.1285
  time to fit residues: 265.3656
Evaluate side-chains
  197 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 153
  time to evaluate  : 1.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  985 MET
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1212 ILE
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   89 ASP
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   67 GLU
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  231 ILE
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  381 ILE
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 137 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 106 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 116 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 156 optimal weight:    3.9990
   chunk 134 optimal weight:    0.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 398 GLN
A 550 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.182021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.128162 restraints weight = 42603.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 4.80
r_work: 0.3402 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14978  Z= 0.170
  Angle     :  0.651  14.917  20470  Z= 0.332
  Chirality :  0.044   0.196   2228
  Planarity :  0.005   0.065   2497
  Dihedral  : 16.343 147.482   2303
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.12 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 26.17 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.20), residues: 1713
  helix:  1.15 (0.20), residues: 666
  sheet:  0.51 (0.33), residues: 238
  loop : -1.79 (0.21), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 748 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.021   0.002   PHE A 610 
 TYR   0.025   0.002   TYR C 206 
 ARG   0.010   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03840 (  614)
  hydrogen bonds       : angle       4.83847 ( 1723)
  covalent geometry    : bond        0.00397 (14978)
  covalent geometry    : angle       0.65073 (20470)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 165
  time to evaluate  : 1.558 
Fit side-chains
REVERT: A  108 GLN cc_start: 0.6939 (tt0) cc_final: 0.6205 (mt0)
REVERT: A  183 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5927 (pm20)
REVERT: A  372 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6613 (mt-10)
REVERT: A  780 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.7042 (pt0)
REVERT: A  947 LYS cc_start: 0.5794 (tptt) cc_final: 0.5076 (ttmt)
REVERT: A 1121 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7582 (tm-30)
REVERT: B  256 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8032 (tp)
REVERT: B  394 GLU cc_start: 0.8022 (tp30) cc_final: 0.7497 (tp30)
REVERT: B  421 MET cc_start: 0.6800 (pp-130) cc_final: 0.6402 (pp-130)
REVERT: C  306 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6944 (mt)
REVERT: C  355 GLN cc_start: 0.4976 (OUTLIER) cc_final: 0.3882 (pm20)
REVERT: C  400 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6918 (tm-30)
REVERT: C  409 ASN cc_start: 0.7685 (m-40) cc_final: 0.7475 (m-40)
  outliers start: 57
  outliers final: 37
  residues processed: 206
  average time/residue: 1.4636
  time to fit residues: 339.5193
Evaluate side-chains
  204 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 159
  time to evaluate  : 4.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  780 GLN
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1206 MET
Chi-restraints excluded: chain A residue 1212 ILE
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   67 GLU
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  162 LEU
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  277 ASP
Chi-restraints excluded: chain C residue  306 LEU
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  381 ILE
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 159 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0970
   chunk 33 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 78 optimal weight:    0.3980
   chunk 160 optimal weight:    0.9980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 398 GLN
A 550 GLN
A 906 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.184564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.132021 restraints weight = 37175.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 4.54
r_work: 0.3449 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14978  Z= 0.131
  Angle     :  0.612  13.899  20470  Z= 0.314
  Chirality :  0.042   0.162   2228
  Planarity :  0.005   0.064   2497
  Dihedral  : 16.285 147.483   2303
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.54 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 26.10 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.20), residues: 1713
  helix:  1.30 (0.21), residues: 663
  sheet:  0.61 (0.34), residues: 232
  loop : -1.74 (0.21), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 918 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.016   0.001   PHE A 766 
 TYR   0.020   0.001   TYR C 206 
 ARG   0.009   0.000   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03488 (  614)
  hydrogen bonds       : angle       4.74352 ( 1723)
  covalent geometry    : bond        0.00294 (14978)
  covalent geometry    : angle       0.61197 (20470)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 167
  time to evaluate  : 1.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6935 (tt0) cc_final: 0.6286 (mt0)
REVERT: A  183 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5887 (pm20)
REVERT: A  372 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6566 (mt-10)
REVERT: A  603 MET cc_start: 0.4364 (OUTLIER) cc_final: 0.4069 (ppp)
REVERT: A  890 ASP cc_start: 0.7992 (p0) cc_final: 0.7658 (p0)
REVERT: A  910 MET cc_start: 0.7894 (mpp) cc_final: 0.7668 (mpt)
REVERT: A  947 LYS cc_start: 0.5810 (tptt) cc_final: 0.5071 (ttmt)
REVERT: A 1121 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7530 (tm-30)
REVERT: A 1131 ILE cc_start: 0.4921 (OUTLIER) cc_final: 0.4148 (mt)
REVERT: B  394 GLU cc_start: 0.8053 (tp30) cc_final: 0.7490 (tp30)
REVERT: B  421 MET cc_start: 0.6723 (pp-130) cc_final: 0.6346 (pp-130)
REVERT: C  355 GLN cc_start: 0.4876 (OUTLIER) cc_final: 0.3803 (pm20)
REVERT: C  400 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6848 (tm-30)
  outliers start: 56
  outliers final: 28
  residues processed: 209
  average time/residue: 1.3536
  time to fit residues: 315.4488
Evaluate side-chains
  191 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 1.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1212 ILE
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  314 MET
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   67 GLU
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  134 LYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  269 SER
Chi-restraints excluded: chain C residue  277 ASP
Chi-restraints excluded: chain C residue  355 GLN
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 45 optimal weight:    0.0970
   chunk 165 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0370
   chunk 93 optimal weight:    0.0670
   chunk 105 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 174 optimal weight:   10.0000
   overall best weight:    0.3394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.187788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.134817 restraints weight = 38705.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 4.08
r_work: 0.3513 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3524
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3524
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14978  Z= 0.117
  Angle     :  0.595  13.920  20470  Z= 0.304
  Chirality :  0.041   0.162   2228
  Planarity :  0.005   0.064   2497
  Dihedral  : 16.225 147.027   2301
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.07 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 27.13 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.21), residues: 1713
  helix:  1.38 (0.21), residues: 670
  sheet:  0.70 (0.34), residues: 232
  loop : -1.68 (0.21), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 918 
 HIS   0.005   0.001   HIS C  77 
 PHE   0.018   0.001   PHE A 766 
 TYR   0.018   0.001   TYR C 206 
 ARG   0.024   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  614)
  hydrogen bonds       : angle       4.66266 ( 1723)
  covalent geometry    : bond        0.00257 (14978)
  covalent geometry    : angle       0.59494 (20470)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 168
  time to evaluate  : 1.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6973 (tt0) cc_final: 0.6184 (mt0)
REVERT: A  120 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8637 (mp)
REVERT: A  183 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6106 (pm20)
REVERT: A  372 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6445 (mt-10)
REVERT: A  603 MET cc_start: 0.4496 (OUTLIER) cc_final: 0.4116 (ppp)
REVERT: A  890 ASP cc_start: 0.8006 (p0) cc_final: 0.7647 (p0)
REVERT: A  910 MET cc_start: 0.7930 (mpp) cc_final: 0.7696 (mpt)
REVERT: A  947 LYS cc_start: 0.5862 (tptt) cc_final: 0.5112 (ttmt)
REVERT: A 1121 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7395 (tm-30)
REVERT: A 1131 ILE cc_start: 0.4799 (OUTLIER) cc_final: 0.4025 (mt)
REVERT: A 1218 LEU cc_start: 0.7807 (pp) cc_final: 0.7535 (pp)
REVERT: B   75 ARG cc_start: 0.6578 (mmm160) cc_final: 0.6235 (mpp-170)
REVERT: B  124 GLN cc_start: 0.5776 (mm-40) cc_final: 0.5431 (mm-40)
REVERT: B  394 GLU cc_start: 0.8084 (tp30) cc_final: 0.7732 (tp30)
REVERT: B  421 MET cc_start: 0.6564 (pp-130) cc_final: 0.6319 (pp-130)
REVERT: B  460 THR cc_start: 0.7972 (p) cc_final: 0.7669 (p)
REVERT: C  400 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6877 (tm-30)
  outliers start: 40
  outliers final: 21
  residues processed: 197
  average time/residue: 1.2157
  time to fit residues: 264.9341
Evaluate side-chains
  188 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 1.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   67 GLU
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 173 optimal weight:   10.0000
   chunk 112 optimal weight:    0.9990
   chunk 120 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 169 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.185085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.132177 restraints weight = 37083.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 3.98
r_work: 0.3467 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14978  Z= 0.146
  Angle     :  0.627  15.160  20470  Z= 0.317
  Chirality :  0.043   0.209   2228
  Planarity :  0.005   0.079   2497
  Dihedral  : 16.301 147.079   2301
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.71 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 27.75 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.21), residues: 1713
  helix:  1.42 (0.21), residues: 657
  sheet:  0.69 (0.34), residues: 232
  loop : -1.61 (0.21), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 918 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.015   0.001   PHE A 766 
 TYR   0.018   0.002   TYR C 206 
 ARG   0.017   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  614)
  hydrogen bonds       : angle       4.72796 ( 1723)
  covalent geometry    : bond        0.00337 (14978)
  covalent geometry    : angle       0.62692 (20470)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3426 Ramachandran restraints generated.
    1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 164
  time to evaluate  : 1.623 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.6996 (tt0) cc_final: 0.6353 (mt0)
REVERT: A  120 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8641 (mp)
REVERT: A  183 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.6071 (pm20)
REVERT: A  222 SER cc_start: 0.7333 (m) cc_final: 0.6919 (p)
REVERT: A  372 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6480 (mt-10)
REVERT: A  603 MET cc_start: 0.4502 (OUTLIER) cc_final: 0.4159 (ppp)
REVERT: A  890 ASP cc_start: 0.7961 (p0) cc_final: 0.7619 (p0)
REVERT: A  947 LYS cc_start: 0.5873 (tptt) cc_final: 0.5119 (ttmt)
REVERT: A 1121 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7496 (tm-30)
REVERT: B   75 ARG cc_start: 0.6699 (mmm160) cc_final: 0.6280 (mpp-170)
REVERT: B  124 GLN cc_start: 0.5860 (mm-40) cc_final: 0.5496 (mm-40)
REVERT: B  394 GLU cc_start: 0.8100 (tp30) cc_final: 0.7762 (tp30)
REVERT: B  421 MET cc_start: 0.6594 (pp-130) cc_final: 0.6315 (pp-130)
REVERT: B  460 THR cc_start: 0.8018 (p) cc_final: 0.7747 (p)
REVERT: C  201 ASN cc_start: 0.7262 (OUTLIER) cc_final: 0.6923 (t160)
REVERT: C  397 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6682 (mp10)
REVERT: C  400 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6901 (tm-30)
  outliers start: 36
  outliers final: 24
  residues processed: 191
  average time/residue: 1.3175
  time to fit residues: 277.9909
Evaluate side-chains
  196 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 164
  time to evaluate  : 1.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  372 GLU
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain A residue  819 SER
Chi-restraints excluded: chain A residue  885 THR
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1131 ILE
Chi-restraints excluded: chain A residue 1136 GLU
Chi-restraints excluded: chain A residue 1227 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain B residue  368 HIS
Chi-restraints excluded: chain B residue  383 VAL
Chi-restraints excluded: chain B residue  396 ARG
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain C residue   67 GLU
Chi-restraints excluded: chain C residue   93 SER
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  201 ASN
Chi-restraints excluded: chain C residue  238 SER
Chi-restraints excluded: chain C residue  261 GLN
Chi-restraints excluded: chain C residue  397 GLN
Chi-restraints excluded: chain C residue  400 GLN
Chi-restraints excluded: chain C residue  407 LEU
Chi-restraints excluded: chain C residue  413 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 176
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 157 optimal weight:    2.9990
   chunk 141 optimal weight:    0.7980
   chunk 69 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 144 optimal weight:    1.9990
   chunk 174 optimal weight:   10.0000
   chunk 172 optimal weight:    0.5980
   chunk 134 optimal weight:    0.0870
   overall best weight:    0.5158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.186823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.134878 restraints weight = 30928.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 3.67
r_work: 0.3508 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3526
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14978  Z= 0.124
  Angle     :  0.608  14.896  20470  Z= 0.308
  Chirality :  0.042   0.182   2228
  Planarity :  0.005   0.069   2497
  Dihedral  : 16.226 147.068   2298
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.48 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 27.34 %
    Favored  : 69.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.21), residues: 1713
  helix:  1.42 (0.21), residues: 663
  sheet:  0.69 (0.34), residues: 232
  loop : -1.68 (0.21), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 918 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.017   0.001   PHE A 766 
 TYR   0.017   0.001   TYR C 206 
 ARG   0.016   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03377 (  614)
  hydrogen bonds       : angle       4.68352 ( 1723)
  covalent geometry    : bond        0.00278 (14978)
  covalent geometry    : angle       0.60779 (20470)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13065.45 seconds
wall clock time: 230 minutes 29.11 seconds (13829.11 seconds total)